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CV E. Koonin

EUGENE V KOONIN, PhD

CURRICULUM VITAE AND BIBLIOGRAPHY

Senior Investigator

National Center for Biotechnology Information, National Library of  Medicine, National Institutes of Health, Bldg. 38A, 8600 Rockville Pike,

Bethesda, MD 20894; Fax (301)480-9241; Telephone (301)435-5913

email koonin@ncbi.nlm.nih.gov

url: http://www.ncbi.nlm.nih.gov/CBBresearch/Koonin/

Home address: 5427 Whitley Park Terrace, Bethesda, MD 20814

Telephone (301)564-1546

PRINCIPAL RESEARCH DIRECTIONS

  • Evolutionary systems biology: emergence and evolution of genomic and organizational complexity in biological systems.
    Comparative analysis of sequenced genomes and automatic methods for genome-scale annotation of gene functions.
  • Application of comparative genomics for phylogenetic analysis, reconstruction of ancestral life forms and building large-scale evolutionary scenarios.
  • Mathematical modeling of genome evolution.
  • Comparative-genomic study of the major transitions in the evolution of life, such as the origin of eukaryotes.
  • Origin of cells and viruses.
  • Origin and evolution of viruses infecting eukaryotes.
  • Evolution of eukaryotic signaling and developmental pathways from the comparative-genomic perspective.
  • Testing fundamental predictions of evolutionary theory, in particular, the relationship between neutral evolution and various modes of selection, using genome-wide sequence comparison.
  • Developing a general theory of evolution using principles and models of statistical physics.

EDUCATION AND TRAINING

1973-1978 Virology department, School of Biology, Moscow State University

Biology diploma /equiv.of  M.Sc./,  1978

Summa cum laude

Supervisor: Professor V. I. Agol

"A comparative  study  on  the  UV  resistance  of single-stranded and  double-stranded RNA of  encephalomyocarditis virus: Evaluation of the possible contribution of host-mediated  repair".

PhD - Department of Biology, Moscow State University, 1983

 Supervisor: Professor V. I. Agol

"Multienzyme organization of encephalomyocarditis virus replication complexes"

PROFESSIONAL EXPERIENCE:

1996-present Senior Investigator, National Center for Biotechnology Information, National Library of Medicine,  N.I.H., Bethesda, MD

2002-2008 Adjunct Professor, Department of Biology, Georgia Institute of Technology, Atlanta, GA

2002-present Adjunct Professor of Bioinformatics, Program in Bioinformatics, Boston University, Boston, MA

11/15/1991-1996 Visiting Scientist, National Center for Biotechnology Information, National Library of Medicine,  N.I.H., Bethesda, MD

02/1991-05/1991 Visiting Scientist, Biology Department, Texas A&M University, College Station, TX

1990-1991  Chief,  Laboratory of Gene Systematics and Bacterial Evolution, Institute of Microbiology, USSR Academy of Sciences

1989-1990 Senior Research Scientist, Laboratory of Bacterial Genetics, Institute of Microbiology, USSR Academy of Sciences

1986-1988 Senior Research Scientist, Laboratory of Virus Biochemistry, Institute of Poliomyelitis, USSR Academy of Medical Sciences

1983-1985 Research Scientist, Laboratory of Virus Biochemistry, Institute of Poliomyelitis, USSR Academy of Medical Sciences

Teaching experience and supervision of other scientists:

April 2005 - Lecture course on "Computational Genomics", Boston University

November 2003 - Lecture course on "Computational Approaches in Comparative Genomics", Georgia Institute of Technology, Atlanta, GA

November 2002 - Lecture course on "Computational Approaches in Comparative Genomics", Georgia Institute of Technology, Atlanta, GA

December 1998 - Lecture course on "Computational Biology and Genome Analysis", Moscow State University, Moscow, Russia

1997 - present - supervision of a group including 5 Staff Scientists, 4-10 Postdoctoral Fellows and 5-15 bioinformatics analysts at the National Center for Biotechnology Information (NIH)

1993 - 1996 - supervision of 2-3 Postdoctoral Fellows at the National Center for Biotechnology Information (NIH)

1990-1991 - supervision of a laboratory staff of 7 scientists at the Institute of Microbiology, USSR Academy of Sciences

Honors, awards, chairmanships

2009 - Fellow, Institute of Biology, UK

2008, Co-Organizer, Aspen Workshop in Physics "From Atoms to Organisms"

2007   Chair, Gordon Research Conference on           "Structural, Functional and Evolutionary Genomics" (Hinxton, Cambridge, UK)

2005 Vice-Chair, Gordon Research Conference on           "Structural, Functional and Evolutionary Genomics" (Bates College, Maine)

2005   Co-organizer, International Workshop on Complex biomolecular networks: structure, evolution, and function (Montauk, NJ)

2001- Fellow of the American College of Medical Informatics

1999  National Library of Medicine Board of Regents' Award

  • 1999 Guest Editor, Current Opinions in Genetics and Development - "Genomes and Evolution"

1999 Co-organizer, Cold Spring Harbor Laboratory Workshop on Computational Biology "Bridging the Gap Between Sequence and Function" , Cold Spring Harbor, Sept 7-9

1997, 1999, 2001, 2003, 2005 Co-Chair, Conference on "In Silico Biology", Atlanta, GA.

1995 - Georgia Institute of Technology Phi-Beta-Kappa Award for the best research paper of the year

1993 - 1999.  Member of the Executive Committee, International Committee for Taxonomy of Viruses

1992. Guest Editor, Seminars in Virology - "Evolution of Viral Genomes"

Editorship, editorial boards and peer review
2005- present Editor-in-Chief, Biology Direct (a new Current Science Group journal with open peer review)

2009-present Associate Editor, Genome Biology and Evolution

2005- present Editorial Advisor, Gene

1998-2008 Editor of the "Genome  Analysis" section, Trends in Genetics

2001- present Associate Editor, Archaea

1997-2004 Associate Editor, In silico Biology

2008-present Editorial Board, Journal of Biology

2002- present Editorial Board, Cell Cycle

2003 - presentEditorial Board, RNA Biology

2000 - present Editorial Board, Nucleic Acids Research

2000- presentEditorial Board, Genome Biology

1999 - 2001 Editorial Board, Bioinformatics

2001-2003Editorial Board, Molecular and Cellular Proteomics

Ad hoc Guest Editor - PNAS, PLOS Biol

Peer review of manuscripts for Nature, Nature Genetics, Science, Cell, PNAS, Trends Biochem. Sci., J. Mol. Biol., Nucleic Acids Res., Proteins etc.


Professional Affiliations

American Society for Microbiology (1992); American Society for Virology (1992); American Association for the Advancement of Science (1992); New York Academy of Sciences (1993).

Invited lectures (a small selection from major meetings in 2004-2008)

June 2008 American Society of Microbiology General Meeting, Toronto, Canada

Colloquium lecture "Big Bangs of viral evolution"

May 2008, Rockefeller University, New York, Evolution Symposium. Lecture "The Origin of Eukaryotes".

June 2007, Society for Molecular Biology and Evolution General meeting, Halifax, Canada, Symposium lecture "Evolution of eukaryotic introns"

September 2006, Fondation Les Treilles Meeting on The Last Universal Cellular Ancestor, Tourtour, France; lecture: "The viral scenario of the origin of cellular life"

June 2006 American Society of Microbiology General Meeting, Toronto, Canada

Symposium lectures "Minimal gene sets of prokaryotes" and "Evolutionary genomics of lactobacilli"

May 2006, Society for Molecular Biology and Evolution General meeting, Tempe, Arizona, Symposium lecture "Evolutionary systems biology"

June 2005, 14th Albany Conversation (Albany, NY)

Plenary  lecture "Universal and lineage-specific trends in protein evolution"

February 2005, Gordon Research Conference on DNA Repair (Ventura, CA)

Keynote lecture "Evolution of eukaryotic DNA repair"

July 2004, Fondation Les Treilles Meeting on Origin and Evolution of the Eukaryotic Nucleus, Tourtour, France

Lectures: "Ancestral eukaryotic gene duplications" and "Evolution of the nuclear pore complex"

June 2004, Society for Molecular Biology and Evolution General meeting, Pennsylvania State University, Symposium lecture "Universal Trends in Protein Evolution"

 

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